A magnetic resonance (MR) stage microscope combines the convenience and flexibility of an optical stage microscope with the unique strengths of magnetic resonance imaging, particularly the ability to image the internal structure of optically opaque organisms and samples. Magnetic resonance microscopy is typically defined as MR imaging with a spatial resolution less than approximately 100 microns. Most MR microscopy employs cylindrical gradient and radiofrequency (RF) coils which entirely or partially enclose an object. RF coils transmit signal to and receive signal from the resonant nuclei in the sample. Resonant frequencies at the magnetic field strengths used for nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) (typically between 0.1 Tesla and 20 Tesla) are in the RF range. The gradient coils create linear, spatial variations in the magnetic field. When combined with the linear relation between magnetic field strength and resonance frequency, the position in space of a resonant nucleus (such as the proton nucleus of a hydrogen atom) can be determined by frequency analysis of the detected signal. This “frequency encoding” of position is fundamental to image formation in MRI. Typically, gradient coils provide independent linear magnetic field gradients in the x, y and z dimensions. This places severe restrictions on the dimensions of a sample and of the environment volume available for a living organism.